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Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide inhibitor.
Analyse Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P8W
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, O67, CA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 169 | 37% helix, 27% strand | P01116 |
| B | GTPase KRAS | protein | 168 | 36% helix, 27% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- O67 · N-(5-bromo-2-{2-oxo-2-[(1-propanoylazetidin-3-yl) amino]ethoxy}phenyl)-3-methyl-1,2-oxazole-5-carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.67 | 0.81 | 46 | CA, GDP, O67 |
| 2 | 330 | 0.64 | 0.80 | 44 | CA, GDP, O67 |
| 3 | 148 | 0.57 | 0.82 | 26 | empty |
| 4 | 116 | 0.43 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6P8W · Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01116
- Elsewhere: RCSB PDB 6P8W · PDBe 6P8W · UniProt P01116
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